In Preview 3 this link does take you to the "front page" Moodle files that are public as would be expected behavior (see screen shot). I am not sure if this was a bug in Preview 2 or if they functionality had not been added in yet.
The direct link to the site files is only accessible to an authenticated administrator. Although non-admin users and non-authenticated users can navigate to directly to a file if they can guess the URL, they can not pull up the directory. They will receive an error message regarding permissions. This was tested on Preview 3 (Build: 20100608).
As for the course files there are major changes in 2.0. The files that are associated with the course activities can be added a number of new ways. Moodle builds a directory structure for each activity. I assume that this is to better support the ability to export activities and resources with out having to export all of the course files. With this new structure the files become managed within the activity or the resource. In addition there is also personal files that are associated with each user. Personal files allows for the user to upload files to a personal repository via the Private files block that can be added to any course. These files can then be added to multiple courses via the repository navigation in the resources and activities that you are linking.
The course backup features have not been fully implemented yet so we are still waiting to see how the backup process will handle the files and the private files that are used in a course.